I recently had the same issue with the jSignature plugin and my Knockout view. I needed the KO view to have fully rendered before I invoked jSignature, otherwise it didn't size itself correctly.
I fixed it with a template binding and an afterRender callback function to invoke the jQuery work.
Here's the KO docs:
http://knockoutjs.com/documentation/template-binding.html
Here's a quick jsfiddle showing how you can use it:
http://jsfiddle.net/PCbFZ/
The trick is that you can use the afterRender callback of the template binding without actually using a template itself. Instead, you wrap all your existing HTML in a div that will invoke the afterRender callback:
<div data-bind="template: {afterRender: initApp}">
<!-- your existing HTML here -->
</div>
initApp is the function that does the jQuery work.
I think that should generally do what you need, though if your HTML is particularly complex, or you have many views you need to render inside the one page, you might need to do a bit more work. Let me know how you get on - maybe I can try to help a bit more if this doesn't quite fix your issue as easily as it did mine!
Update - following the comment from JACL below - here's an extended version of the fiddle showing this technique also working with ko-if. Each time you show/hide the 'widget' using the checkbox, a different random colour is applied to indicate the afterRender function doing its work.
http://jsfiddle.net/PCbFZ/15/
ko.applyBindings()
inside$(document).ready()
? – Quarles